Variant chr17-80038043-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The NM_017950.4(CCDC40):c.30-80G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.129 in 887,852 control chromosomes in the GnomAD database, including 7,893 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.13 ( 1281 hom., cov: 31)

Exomes 𝑓: 0.13 ( 6612 hom. )

Consequence

CCDC40
NM_017950.4 intron

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.733

Variant links:

Genes affected

CCDC40 (HGNC:26090): (coiled-coil domain 40 molecular ruler complex subunit) This gene encodes a protein that is necessary for motile cilia function. It functions in correct left-right axis formation by regulating the assembly of the inner dynein arm and the dynein regulatory complexes, which control ciliary beat. Mutations in this gene cause ciliary dyskinesia type 15, a disorder due to defects in cilia motility. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2011]

CCDC40 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.92).

BP6

Variant 17-80038043-G-A is Benign according to our data. Variant chr17-80038043-G-A is described in ClinVar as [Benign]. Clinvar id is 1281104.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE
CCDC40	NM_017950.4 linkuse as main transcript	c.30-80G>A	intron_variant	ENST00000397545.9
CCDC40	NM_001243342.2 linkuse as main transcript	c.30-80G>A	intron_variant
CCDC40	NM_001330508.2 linkuse as main transcript	c.30-80G>A	intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CCDC40	ENST00000397545.9 linkuse as main transcript	c.30-80G>A		intron_variant		5	NM_017950.4	P2	Q4G0X9-1

Frequencies

GnomAD3 genomes

AF:

0.126

AC:

19101

AN:

151962

Hom.:

1283

Cov.:

show subpopulations

Gnomad AFR

AF:

0.120

Gnomad AMI

AF:

0.0274

Gnomad AMR

AF:

0.0771

Gnomad ASJ

AF:

0.124

Gnomad EAS

AF:

0.164

Gnomad SAS

AF:

0.115

Gnomad FIN

AF:

0.163

Gnomad MID

AF:

0.169

Gnomad NFE

AF:

0.133

Gnomad OTH

AF:

0.128

GnomAD4 exome

AF:

0.129

AC:

95108

AN:

735770

Hom.:

6612

Cov.:

AF XY:

0.130

AC XY:

50678

AN XY:

389552

show subpopulations

Gnomad4 AFR exome

AF:

0.119

Gnomad4 AMR exome

AF:

0.0669

Gnomad4 ASJ exome

AF:

0.123

Gnomad4 EAS exome

AF:

0.182

Gnomad4 SAS exome

AF:

0.130

Gnomad4 FIN exome

AF:

0.167

Gnomad4 NFE exome

AF:

0.127

Gnomad4 OTH exome

AF:

0.126

GnomAD4 genome

AF:

0.126

AC:

19099

AN:

152082

Hom.:

1281

Cov.:

AF XY:

0.127

AC XY:

9419

AN XY:

74354

show subpopulations

Gnomad4 AFR

AF:

0.120

Gnomad4 AMR

AF:

0.0770

Gnomad4 ASJ

AF:

0.124

Gnomad4 EAS

AF:

0.164

Gnomad4 SAS

AF:

0.115

Gnomad4 FIN

AF:

0.163

Gnomad4 NFE

AF:

0.133

Gnomad4 OTH

AF:

0.128

Alfa

AF:

0.126

Hom.:

1797

Bravo

AF:

0.117

Asia WGS

AF:

0.128

AC:

445

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

Jul 09, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.10

DANN

Benign

0.33

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over